merge refactor

.editorconfig

@@ -0,0 +1,21 @@
+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

.github/workflows/python-app.yml

@@ -0,0 +1,32 @@
+name: Python Package
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        pip install tox tox-gh-actions
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with tox
+      run: tox

.github/workflows/python-publish.yml

@@ -1,11 +1,16 @@
 # This workflow will upload a Python Package using Twine when a release is created
 # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
 
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
 name: Upload Python Package
 
 on:
   release:
-    types: [created]
+    types: [published]
 
 jobs:
   deploy:
@@ -21,11 +26,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -1,12 +1,3 @@
-# Mac
-.DS_Store
-
-# Latex documentation
-*.aux
-*.fls
-*.fdb_latexmk
-*.log
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -29,6 +20,7 @@ lib64/
 parts/
 sdist/
 var/
+wheels/
 *.egg-info/
 .installed.cfg
 *.egg
@@ -51,8 +43,9 @@ htmlcov/
 .cache
 nosetests.xml
 coverage.xml
-*,cover
+*.cover
 .hypothesis/
+.pytest_cache/
 
 # Translations
 *.mo
@@ -70,13 +63,12 @@ instance/
 .scrapy
 
 # Sphinx documentation
-_build
-_templates
+docs/_build/
 
 # PyBuilder
 target/
 
-# IPython Notebook
+# Jupyter Notebook
 .ipynb_checkpoints
 
 # pyenv
@@ -85,19 +77,33 @@ target/
 # celery beat schedule file
 celerybeat-schedule
 
+# SageMath parsed files
+*.sage.py
+
 # dotenv
 .env
 
 # virtualenv
-.venv/
+.venv
 venv/
 ENV/
 
 # Spyder project settings
 .spyderproject
+.spyproject
 
 # Rope project settings
 .ropeproject
 
-# pycharm
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# IDE settings
+.vscode/
 .idea
+
+# Mac
+.DS_Store

.readthedocs.yaml

@@ -0,0 +1,18 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+   - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+   version: "3.7"

AUTHORS.rst

@@ -0,0 +1,14 @@
+=======
+Credits
+=======
+
+Development Lead
+----------------
+
+* Jacob Reinhold <jcreinhold@gmail.com>
+
+Contributors
+------------
+
+* Sarthak Pati
+* Jakub Kaczmarzyk

CONTRIBUTING.rst

@@ -0,0 +1,126 @@
+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/jcreinhold/intensity-normalization/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+intensity-normalization could always use more documentation, whether as part of the
+official intensity-normalization docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/jcreinhold/intensity-normalization/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `intensity-normalization` for local development.
+
+1. Fork the `intensity-normalization` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:your_name_here/intensity-normalization.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv intensity-normalization
+    $ cd intensity-normalization/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the
+   tests, including testing other Python versions with tox::
+
+    $ flake8 intensity_normalization tests
+    $ python setup.py test or pytest
+    $ tox
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 3.6, 3.7, 3.8, and 3.9.
+
+Tips
+----
+
+To run a subset of tests::
+
+$ pytest tests.test_intensity_normalization
+
+
+Deploying
+---------
+
+A reminder for the maintainers on how to deploy.
+Make sure all your changes are committed (including an entry in HISTORY.rst).
+Then run::
+
+$ bump2version patch # possible: major / minor / patch
+$ git push
+$ git push --tags
+
+Travis will then deploy to PyPI if tests pass.